[Chimera-users] Chimera comands

Tom Goddard goddard at sonic.net
Thu Nov 16 10:24:11 PST 2017

There is not a command equivalent of Volume Viewer / Features / Coordinates / Rotation axis + angle.  But that is not the usual way of moving a map (e.g. for fitting).  That changes the mapping of map grid indices (i,j,k) into physical space (x,y,z).  But there is another positioning matrix that every Chimera model has that transforms its physical space coordinates into the world coordinates.  Almost always you change this second transform, and that is done with move and turn commands using the "models" option of those commands to specify which model you want to shift or rotate.


> On Nov 16, 2017, at 4:19 AM, Michał Kadlof  wrote:
> Thank you for your answer, it almost covers my needs.
> Maybe I was not precise. When I was asking about rotation I mean the same effect when I modify field angle in Volume Viewer -> Features -> Cooridnates. Is it possible in command line?
> --
> pozdrawiam serdecznie
> Michał Kadlof <m.kadlof at cent.uw.edu.pl <mailto:m.kadlof at cent.uw.edu.pl>>
> 2017-11-14 22:17 GMT+01:00 Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>:
> Hi Michał,
> Yes, it’s a little tricky finding commands for some of those things.
> (1) open trajectory would just be done with “open” but you have to use a metafile, which is a text file listing the input file(s) as well as any other parameters that would be required inputs if you were using the MD Movie GUI.  Examples and explanation:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#metafile <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#metafile>>
> (2) there is no command to open a generic pseudobond file, just the PseudoBond Reader tool (in menu under Tools… Depiction).  However, you can either have python to open it, or instead use a bunch of “distance” commands to add distance monitor pseudobonds.  You can control their colors etc. with “setattr,” for example:
> distance :53.a at ca :58.a at ca
> setattr p label ''
> setattr p color dodger blue
> setattr g lineType 1
> setattr g lineWidth 3
> If you select any pseudobond and then show the Selection Inspector by clicking the green magnifying glass, you can see in the dialog which attributes are of the pseudobond (“p” in setattr) or pseudobond group (“g”) and (by mouseover in the dialog) its name and values that could be used in the setattr command.  You can put atomspecs at the ends of those setattr commands to only affect certain pseudobonds instead of all pseudobonds.
> The label command has two single quotation marks (not a single double quotation mark). You could also use two double quotation marks, but be sure to type in the plain ones… my e-mail app insists on changing them to fancy open and close quotation marks, which won’t work.
> (3) The “volume” command includes options to change origin and voxel size.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions>>
> (4) You can rotate a model with “turn” or “roll”.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Nov 14, 2017, at 1:41 AM, Michał Kadlof <m.kadlof at cent.uw.edu.pl <mailto:m.kadlof at cent.uw.edu.pl>> wrote:
> >
> > Hello,
> > I have some troubles with finding in documentation suitable commands.
> >
> > How do I should write script which:
> > - open a trajectory in saved PDB or PSF/DCD in MD movie tool.
> > - read pseudobonds from file, and change the color of all of them at once
> > - change origin, voxel size and rotation angle of opened volumetric data
> >
> > Can you help me?
> > --
> > ​best wishes,
> > Michał Kadlof <m.kadlof at cent.uw.edu.pl <mailto:m.kadlof at cent.uw.edu.pl>>
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